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comparison assembly_post_processor.xml @ 16:1e639e679f61 draft

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author greg
date Mon, 13 Feb 2017 07:40:02 -0500
parents ff5c714e01d1
children 63a4a0f127da
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15:ff5c714e01d1 16:1e639e679f61
20 #if str($prediction_method_cond.prediction_method) == 'estscan': 20 #if str($prediction_method_cond.prediction_method) == 'estscan':
21 --score_matrices '$score_matrices' 21 --score_matrices '$score_matrices'
22 #end if 22 #end if
23 #if str($options_type.options_type_selector) == 'advanced': 23 #if str($options_type.options_type_selector) == 'advanced':
24 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 24 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
25 #set scaffold_path = $options_type.target_gene_family_assembly_cond.scaffold.fields.path 25 #set scaffold = $options_type.target_gene_family_assembly_cond.scaffold.fields.path
26 #set scaffold_dir = $os.path.split($scaffold_path)[0]
27 #set scaffold = $os.path.split($scaffold_path)[1]
28 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups' 26 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
29 --scaffold_dir '$scaffold_dir'
30 --scaffold '$scaffold' 27 --scaffold '$scaffold'
31 --method '$options_type.target_gene_family_assembly_cond.method' 28 --method '$options_type.target_gene_family_assembly_cond.method'
32 #end if 29 #end if
33 --gap_trimming $options_type.gap_trimming 30 --gap_trimming $options_type.gap_trimming
34 #if str($options_type.strand_specific) == 'yes': 31 #if str($options_type.strand_specific) == 'yes':
103 <param name="input" value="assembly.fasta" ftype="fasta" /> 100 <param name="input" value="assembly.fasta" ftype="fasta" />
104 <param name="prediction_method" value="transdecoder" /> 101 <param name="prediction_method" value="transdecoder" />
105 <output_collection name="transcripts" type="list"> 102 <output_collection name="transcripts" type="list">
106 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/> 103 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
107 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/> 104 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
108 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/> 105 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
109 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/> 106 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
110 </output_collection> 107 </output_collection>
111 </test> 108 </test>
112 <test> 109 <test>
113 <param name="input" value="assembly.fasta" ftype="fasta" /> 110 <param name="input" value="assembly.fasta" ftype="fasta" />
115 <param name="options_type_selector" value="advanced" /> 112 <param name="options_type_selector" value="advanced" />
116 <param name="gap_trimming" value="0.1" /> 113 <param name="gap_trimming" value="0.1" />
117 <param name="dereplicate" value="yes" /> 114 <param name="dereplicate" value="yes" />
118 <param name="min_length" value="200" /> 115 <param name="min_length" value="200" />
119 <output_collection name="transcripts" type="list"> 116 <output_collection name="transcripts" type="list">
120 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/> 117 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
121 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/> 118 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
122 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/> 119 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
123 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/> 120 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
124 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/> 121 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
125 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/> 122 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
126 </output_collection> 123 </output_collection>
127 </test> 124 </test>
128 </tests> 125 </tests>
129 <help> 126 <help>
130 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 127 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
137 134
138 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder. 135 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
139 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms. 136 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
140 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble. 137 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
141 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble. 138 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
142 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 139 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the [Data Manager PlantTribes Scaffolds Downloader tool](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_plant_tribes_scaffolds_downloader/4c96b684f0fd).
143 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 140 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
144 * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0] 141 * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
145 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library. 142 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
146 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions. 143 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
147 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions. 144 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.